In 2368, Opaka revealed the location of a resistance cell in Bajor's Kendra Valley, which her own son was a member of, resulting in the deaths of her own son and the 42 other members of the resistance cell. This was in order to keep the Cardassians from killing over 1,000 other Bajorans. Years later, VedekBareil Antos felt compelled to protect her memory by trying to take the blame for the deaths of the resistance cell himself. (DS9: "The Collaborator")

Later that year the Redemptorists leader Hören Rygis set his plan to murder Kira Nerys in motion. The plan resulted in both DoctorJulian Bashir and MajorKira Nerys being cut off from assistance from the station. Kira was trapped on a substation with Hören on board, and Doctor Bashir was trapped in the Bajoran wormhole. The Redemptorists had sabotaged the cargo shuttle carrying the substation so that the engines would harm the inhabitants of the wormhole, and they caused the engines to fire in the wormhole. The Prophets responding by collapsing the Alpha Quadrant end of the wormhole, cutting off Bashir and Kira from assistance. During this time, Commander Sisko visited with Opaka to learn if she had any insights into the situation. Opaka advised Sisko that Hören's obsessions and hatred had swept away Hören's sanity. Doctor Bashir was able to convince the Prophets to send him into a distant future where the universe was dead so that he could use the shuttle's engines without harming them. Opaka's meditations had enabled her to visit this realm and she was able to help lead Julian Bashir back from that realm. (DS9 novel: Bloodletter)

In 2369 Opaka died in a runabout crash on a moon in the Gamma Quadrant, the moon was in fact a prison holding two warring tribes - The Ennis and the Nol-Ennis - who were left to fight forever thanks to microbes in the moons atmosphere with the ability to bring the dead back to life. These microbes allowed Opaka to come back from the dead but also resulting in her having to stay on the moon as leaving would kill her again. Opaka took this as a sign from the Prophets and stayed on the moon to reconcile the warring factions, relinquishing the kaiship. (DS9: "Battle Lines")